Public Member Functions
	Alignment ()

float	getExtend ()

void	setExtend (float extend)

Matrix	getMatrix ()

void	setMatrix (Matrix matrix)

String	getName1 ()

void	setName1 (String name1)

String	getName2 ()

void	setName2 (String name2)

float	getOpen ()

void	setOpen (float open)

float	getScore ()

void	setScore (float score)

int	getLength ()

char[]	getSequence1 ()

void	setSequence1 (char[] sequence1)

char[]	getSequence2 ()

void	setSequence2 (char[] sequence2)

int	getStart1 ()

void	setStart1 (int start1)

int	getStart2 ()

void	setStart2 (int start2)

int	getGaps ()

void	setGaps (int gaps)

int	getIdentity ()

float	getPercentIdentity ()

void	setIdentity (int identity)

int	getLongestPerfectMatch ()

int	getLongestUngappedAlignment (int maxMismatches)

char[]	getMarkupLine ()

void	setMarkupLine (char[] markupLine)

int	getSimilarity ()

void	setSimilarity (int similarity)

String	getSummary ()

String	toString ()

float	calculateScore ()

int	getNumberOfMatches ()

int	getNumberOfMatches2 ()

float	getScoreWithNoTerminalGaps ()

boolean	checkScore ()

Sequence	getOriginalSequence1 ()

void	setOriginalSequence1 (Sequence originalSequence1)

Sequence	getOriginalSequence2 ()

void	setOriginalSequence2 (Sequence originalSequence2)

int	getGaps1 ()

int	getGaps2 ()

Static Public Member Functions
static Alignment	add (Alignment a1, Alignment a2)

static Alignment	copy (Alignment alignment)

Static Public Attributes
static final char	GAP = '-'

Detailed Description

Holds the output of a pairwise sequences alignment.

Author: Ahmed Moustafa (ahmed.nosp@m.@use.nosp@m.rs.sf.nosp@m..net)

Constructor & Destructor Documentation

jaligner.Alignment.Alignment ( )

Constructor for Alignment

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Member Function Documentation

static Alignment jaligner.Alignment.add	(	Alignment	a1,
		Alignment	a2
	)

static

Adds this alignment to another alignment, the order is important.

Parameters

a1	The 1st alignment
a2	The 2nd alignment

Returns: the sum of two alignment

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float jaligner.Alignment.calculateScore ( )

Calculate the score of the alignment, not using the score field (the function only uses sequence1, sequence2, matrix and gap penalties).

Returns: the calculated score (By: Bram Minnaert)

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boolean jaligner.Alignment.checkScore ( )

Check if the calculated score matches the field score.

Returns: true if equal, else false. (By: Bram Minnaert)

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static Alignment jaligner.Alignment.copy ( Alignment alignment )

static

Copies an alignment to another alignment.

Parameters

alignment Alignment

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float jaligner.Alignment.getExtend ( )

Returns: Returns the extend.

int jaligner.Alignment.getGaps ( )

Returns: Returns the gaps.

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int jaligner.Alignment.getGaps1 ( )

Returns the number of gaps of the aligned sequence #1

Returns: the number of gaps of the aligned sequence #1

int jaligner.Alignment.getGaps2 ( )

Returns the number of gaps of the aligned sequence #2

Returns: the number of gaps of the aligned sequence #2

int jaligner.Alignment.getIdentity ( )

Returns: Returns the identity.

int jaligner.Alignment.getLength ( )

Returns the length of the alignment

Returns: Alignment length

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int jaligner.Alignment.getLongestPerfectMatch ( )

Returns: The length of the longest contiguous perfect sub-alignment

int jaligner.Alignment.getLongestUngappedAlignment ( int maxMismatches )

Get the length of the longest ungapped sub-alignment with at most a certain number of mismatches

Parameters

maxMismatches Max mismatches

Returns: Length of longest ungapped sub-alignment with at most this many mismatches

char [] jaligner.Alignment.getMarkupLine ( )

Returns: Returns the markupLine.

Matrix jaligner.Alignment.getMatrix ( )

Returns: Returns the matrix.

String jaligner.Alignment.getName1 ( )

Returns: Returns the name1.

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String jaligner.Alignment.getName2 ( )

Returns: Returns the name2.

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int jaligner.Alignment.getNumberOfMatches ( )

int jaligner.Alignment.getNumberOfMatches2 ( )

float jaligner.Alignment.getOpen ( )

Returns: Returns the open.

Sequence jaligner.Alignment.getOriginalSequence1 ( )

Returns original Sequence #1

Returns: original Sequence #1

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Sequence jaligner.Alignment.getOriginalSequence2 ( )

Returns original Sequence #2

Returns: original Sequence #2

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float jaligner.Alignment.getPercentIdentity ( )

Percent identity

Returns: Matches / length

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float jaligner.Alignment.getScore ( )

Returns: Returns the score.

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float jaligner.Alignment.getScoreWithNoTerminalGaps ( )

Calculate the score of the alignment without the terminal gaps.

char [] jaligner.Alignment.getSequence1 ( )

Returns: Returns the sequence1.

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char [] jaligner.Alignment.getSequence2 ( )

Returns: Returns the sequence2.

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int jaligner.Alignment.getSimilarity ( )

Returns: Returns the similarity.

int jaligner.Alignment.getStart1 ( )

Returns: Returns the start1.

int jaligner.Alignment.getStart2 ( )

Returns: Returns the start2.

String jaligner.Alignment.getSummary ( )

Returns a summary for alignment

Returns: String alignment summary

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void jaligner.Alignment.setExtend ( float extend )

Parameters

extend The extend to set.

void jaligner.Alignment.setGaps ( int gaps )

Parameters

gaps	The gaps to set.

void jaligner.Alignment.setIdentity ( int identity )

Parameters

identity The identity to set.

void jaligner.Alignment.setMarkupLine ( char[] markupLine )

Parameters

markupLine The markupLine to set.

void jaligner.Alignment.setMatrix ( Matrix matrix )

Parameters

matrix The matrix to set.

void jaligner.Alignment.setName1 ( String name1 )

Parameters

name1 The name1 to set.

void jaligner.Alignment.setName2 ( String name2 )

Parameters

name2 The name2 to set.

void jaligner.Alignment.setOpen ( float open )

Parameters

open	The open to set.

void jaligner.Alignment.setOriginalSequence1 ( Sequence originalSequence1 )

Parameters

originalSequence1

void jaligner.Alignment.setOriginalSequence2 ( Sequence originalSequence2 )

Parameters

originalSequence2

void jaligner.Alignment.setScore ( float score )

Parameters

score The score to set.

void jaligner.Alignment.setSequence1 ( char[] sequence1 )

Parameters

sequence1 The sequence1 to set.

void jaligner.Alignment.setSequence2 ( char[] sequence2 )

Parameters

sequence2 The sequence2 to set.

void jaligner.Alignment.setSimilarity ( int similarity )

Parameters

similarity The similarity to set.

void jaligner.Alignment.setStart1 ( int start1 )

Parameters

start1 The start1 to set.

void jaligner.Alignment.setStart2 ( int start2 )

Parameters

start2 The start2 to set.

String jaligner.Alignment.toString ( )

Member Data Documentation

final char jaligner.Alignment.GAP = '-'

static

Gap character

The documentation for this class was generated from the following file:

java/jaligner/Alignment.java

Public Member Functions

Static Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation